Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes global epidemics of debilitating disease worldwide. To gain functional insight into the host cellular genes required for virus infection, we performed whole-blood RNA-seq, 37-plex mass cytometry of peripheral blood mononuclear cells (PBMCs), and serum cytokine measurements of acute- and convalescent-phase samples obtained from 42 children naturally infected with CHIKV. Serum/plasma, PAXgene and PBMC were collected from CHIKV-infected patients at acute (day 1-2 post symptom onset) and convalescent (day 15-17 post symptom onset) time points. RNA-seq (PAXgene samples), Luminex (serum/plasma samples) and CyTOF (PBMCs) was used to analyse the immune profile of CHIKV infection in a pediatric cohort from Nicaragua.